tbuckley/cabot-search huggingface dataset:
1512MO Perioperative camrelizumab (C) combined with rivoceranib (R) and chemotherapy (chemo) versus chemo for locally advanced resectable gastric or gastroesophageal junction (G/GEJ) adenocarcinoma: The first interim analysis of a randomized, phase III trial (DRAGON IV)
Authors: C. Li, Y. Zheng, Z. Shi, L. Yang, B. Zhang, Z. Wang, H. Chen, X. Wang, P. Zhao, J. Dong, C. Lian, Q. Zhao, Z. Zheng, A. Zhang, S. Xu, K. Wang, F. Yuan, Y. Tian, K. Yin, Z. Zhu
Journal: Annals of Oncology (2023)
106P The impact of alterations in cancer driver genes and other potentially targetable mutations on progression and overall survival in patients with biliary tract cancer treated on the randomised phase III multicentre BILCAP clinical trial
Authors: V.E. Crolley, R. Guest, A.D. Beggs, E. Jaynes, S. Thorn, J. Herrero, I. Tomlinson, J.W. Valle, J.N. Primrose, J.A. Bridgewater
Journal: Annals of Oncology (2023)
2355P Carcinoembryonic antigen (CEA) expression in human tumors: A tissue microarray study on 15,413 tumors
Authors: K. Jansen, L. Kornfeld, M. Lennartz, N.C. Blessin, S. Rico, S. Kind, V. Reiswich, A.M. Luebke, C. Hube-Magg, E. Bady, F. Büscheck, A. Menz, R. Uhlig, G. Sauter, R. Simon, C. Bernreuther
Journal: Annals of Oncology (2023)
2013P Investigating the clinical relevance of immune checkpoint expression in the peripheral blood of patients with small cell lung cancer (SCLC)
Authors: D. Mavroudis, A. Boumpouli, E. Vorrias, N. Nikolarakou, A.C. Kyriakidou, M.A. Papadaki, S. Agelaki
Journal: Annals of Oncology (2023)
117P Genomic landscape of biliary tract cancers from India show distinct geographic variation
Authors: N. Rohatgi, A. Agarwal, V. Maniar, S. Patil, A. Bahl, S. Advani, P.K. Julka, S. Limaye, A. Kakroo, A. Kumar, M. Javle
Journal: Annals of Oncology (2023)
124P Clinicopathological nomogram for predicting fibroblast growth factor receptor 2 (FGFR2) gene fusion/rearrangement (F/R) in intrahepatic cholangiocarcinoma (iCCA)
Authors: M. Bensi, D. Giannarelli, C. Bagalà, M. Niger, F. Bergamo, D. Barone, M.D. Rizzato, F. Nichetti, A. Spring, A. De Rosa, V. Beccia, G. Ricagno, C.C. Pircher, F. Ardito, B. Barbaro, F. Giuliante, E. Martinelli, F.G.M. De Braud, S. Lonardi, G. Tortora, L. Salvatore
Journal: Annals of Oncology (2023)
2281P Multi-omics evaluation of TFE3-fusions and potential association with immuno-metabolic vulnerabilities in alveolar soft part sarcoma (ASPS) and translocation-positive renal cell carcinoma (tRCC)
Authors: S. Wei, H. Krause, K. Wright, I-M. Schaefer, I. Odintsov, M. Phan, A. Ayanambakkam, W.R. Chen, K. Liu, A. Farrell, N. Soror, A. Elliott, P. Barata, E. Heath, B.A. Carneiro, C. Nabhan, A. Chen, A.E. Rosenberg, D. Geynisman, A-R. Naqash
Journal: Annals of Oncology (2023)
2293P Protumoral role of neutrophils and neutrophils extracellular traps (NETS) in non-metastatic gastroesophageal and rectal cancers
Authors: C. Catozzi, L. Gervaso, L. Benini, D. Ciardiello, M.G. Zampino, F. Spada, M. Borghesani, C. Valenza, L. Algeri, L. Guidi, G. Pellizzari, N. Fazio, L. Nezi, C.A. Cella
Journal: Annals of Oncology (2023)
2291P WU-NK-101, best in class memory-NK cell, has key features vital for adoptive cell therapy (ACT) in solid tumors (ST)
Authors: J. Muth, T. Leedom, K. Magee, B. Muz, J. Vadakekulathu, V. Petit, N. Bhatnagar, D. Primo, P. Comune Pennacchi, M. Berrien-Elliott, T.A. Fehniger, J. Davidson-Moncada, S. Rutella
Journal: Annals of Oncology (2023)
2280P MiR-193a-3p: A pan-repressor of H2S synthesizing enzymes regulates tumorigenesis and immunosurveillance in breast cancer
Authors: A. Dawoud, R.A. Youness, H.M. Nafea, C. Bourquin, C. Szabo, R.M. Abdel-Kader, M. Gad
Journal: Annals of Oncology (2023)
2273P Influence of body mass index (BMI) on the response to chemotherapy in patients with HER2+ breast cancer: Role of the leptin axis
Authors: M. González Rodríguez, M. Fernadez Abad, J. Palacios Calvo, M. Sampayo, I. Calvo, E. Díaz, B. Pérez Míes, S. González Martínez, J. Pérez García, J. Cortés, G. Moreno-Bueno, L. García Estevez
Journal: Annals of Oncology (2023)
2274P Deep learning-based prediction of pathologic complete response to neoadjuvant therapy in breast cancer using H&amp;E images and RNA-Seq in the IMMUcan study
Authors: C. Esposito, A. Joaquin Garcia, M. Rediti, N. Penel, J. Oliveira, J-C. Goeminne, P. Fournel, A. Capela Marques, M. Morfouace, L. Buisseret, H.S. Hong, C. Maussion
Journal: Annals of Oncology (2023)
2266P IMMUcan consortium: Focus on the first results of the non-small cell lung cancer (NSCLC) cohort
Authors: M. Morfouace, D. Schulz, N. Eling, F. Marzetta, C. Loizides, S. Rusakiewicz, R. Liechti, H.S. Hong, M-S. Robert, P. Bironzo, T. Cufer, K. Oselin, N. Cloarec, J. Oliveira, B. Bodenmiller, B. Besse
Journal: Annals of Oncology (2023)
2269P Patient derived xenografts generated from circulating cancer stem cells on chorioallantoic membrane as an alternative pre-clinical model for personalized medicine in pancreatic cancer
Authors: M. Pizon, D. Schott, B.J. Wagner, S. Boscheck, K. Pachmann, T. Aung, C. Hackl, S. Härteis
Journal: Annals of Oncology (2023)
2287P Multiomic Biological mOdifications in the immune response of patients treated with chemotherapy, anti-CD20, or immune-checkpoint inhibitors and receiving a Third dose of vaccinE against SARS-CoV-2 (the BO0STER study)
Authors: G. Zoppoli, L. Ferrando, F. Ravera, M. Dameri, I. Lombardo, M. Stabile, N. Fallani, B. Cigolini, G. Gentilcore, B. Bruzzone, A. Domnich, A. Orsi, F. Ballerini, D. Rinchai, D. Chaussabel, D. Bedognetti, J-C. Grivel, C. Genova, R. Lemoli, A. Ballestrero
Journal: Annals of Oncology (2023)
2275P Circulating leptin and adiponectin levels in premenopausal women with and without breast cancer (BC) and a body mass index (BMI) ≥25 kg/m2
Authors: I. Calvo, M.L. Argente, A. Conde, M. Sampayo, M. González Rodríguez, C. Yelo, V. Corraliza, J. Pérez García, J. Cortés, L. García Estevez
Journal: Annals of Oncology (2023)
2284P Pre-clinical assessment of the therapeutic potential of a CD80-Fc-armed oncolytic virus (VSV-GP-CD80Fc)
Authors: A. Ackermann, P. Erlmann, V.L. Herrmann, D. Hotter, S. Mostböck, T. Nolden, J. Petschenka, T. Schönberger, B. Stierstorfer, J-G. Wojtyniak, K. Elbers, P. Mueller, J. Rippmann
Journal: Annals of Oncology (2023)
2282P Tissue glycan profiling in predicting immunotherapy response in renal cell carcinoma and hepatocelllular carcinoma
Authors: Q.J. Low, W.D. Looi, S.J. Sukumar, Y. Ang, A.S. Wong, R.A. Soo, R. Sundar, J. Lum, C.E. Chee, G. Kunnath Bonney, H.L. Tan, W.P. Yong
Journal: Annals of Oncology (2023)
2286P COVID-19 vaccinations in cancer patients (pts): An individual participant data meta-analysis of the International Consortium on COVID vaccination in cancer
Authors: H.M.L. Le, A.M. Schmitt, S.T.C. Shepherd, A. Bhattacharya, C. Bresee, R.S.N. Fehrmann, S. Oosting, A.A.M. Van der Veldt, K. Reckamp, J.B.A.G. Haanen, E.G.E. de Vries, S. Turajlic
Journal: Annals of Oncology (2023)
2283P Assessing the replicative potential of the oncolytic virus VSV-GP in patient-derived tumor biopsies ex vivo
Authors: B. Schoeps, M. Mayr, M. Glatz, S. Estermann, A. Guerrero Tort, S. Scheidl, C. Knobbe-Thomsen, T. Nolden, S. Schneeberger, K. Elbers, U. Lauer, L. Kloker, S. Berchtold, J. Beil, C. Yurttas, R. Kleemann, M. Petersson
Journal: Annals of Oncology (2023)
2271P Development of an oncolytic virus for the treatment of high grade serous ovarian cancer and other stromal rich tumours
Authors: M. Bazan Peregrino, S.C. Frost, C. Negroni, C. Moriconi, T. Perry, W. Taverner, B. Nicholls, D. Saunders, R. Ackerman-Johnson, P. Cunnea, C. Fotopoulou, J. Krell, A. Lim, K. Fisher, M.R. Duffy
Journal: Annals of Oncology (2023)
2298P Feasibility of ex vivo drug sensitivity testing in urothelial cancer: EVITA trial
Authors: M.P. Scholtes, L. Ceton, D. van der Meer, F. Grillet, M. Garcia Montero, C.Z. Roeland, E. Boevé, J. Leijte, H. Roshani, G.J. van Leenders, W. Vader, J.L. Boormans
Journal: Annals of Oncology (2023)
2295P Pan-cancer prevalence of MET fusions and clinical response to MET- targeted therapy
Authors: M. Vojnic, I. Odintsov, Z. Liu, D. Lu, M. Harshan, A. Ameri, S. Machnicki, X. Xiao, W. Lockwood, M. Ladanyi, R. Somwar
Journal: Annals of Oncology (2023)
2272P Minimal DNA-methylation (DNAm) signatures for non-invasive tumor-agnostic estimation of tumor content (TC) and molecular subtype in patients (pts) with metastatic breast cancer (mBC)
Authors: M. Benelli, A. Nardone, F. Galardi, D. Romagnoli, F. De Luca, S. Gabellini, M. Paoli, I. Migliaccio, M. Pestrin, G. Sanna, E. Risi, L. Livraghi, E. Moretti, C. Biagioni, L. Malorni, L. Biganzoli
Journal: Annals of Oncology (2023)

Non-invasive detection and quantification of circulating tumor DNA by DNAm signatures is emerging as powerful tool for monitoring disease status in pts with metastatic cancer. We recently developed MIMESIS, a computational workflow to design tumor agnostic DNAm signatures of few dozen sites for TC and molecular subtype estimation in liquid biopsy. Here we applied a MIMESIS informed assay to a retrospective cohort of mBC pts (MIMESIS-BC). 72 mBC pts (42 ER+/HER2-, 2 ER+/HER2 N/A, 8 ER+/HER2+, 6 ER-/HER2+, 14 ER-/HER2-, up to 6 previous lines of treatment) and 11 healthy individuals (ctrl) were included. Plasma from mBC pts was collected before starting treatment (T0, n=58) and after the first cycle (T1, n=52) (n=38 pts T0 and T1). MIMESIS-BC for TC, PAM50 molecular subtypes and ER status (n=139 sites) was applied to circulating free DNA as described in the MIMESIS study. Samples were defined as TC+ when TC>0. TC values as continuous variable and TC classes (+/-) were associated with OS and PFS. Concordance of subtype and ER status by MIMESIS-BC with IHC-based from primary tumor was estimated by chi-square and percent agreement. TC was not detected in ctrl. A significantly higher median TC was observed at T0 compared to T1 (5.6% (range 0-73%) vs 0% (range 0-47%); p=0.02). 39 TC+ samples at T0 showed 61% agreement for molecular subtype (p=0.002) and 86% for ER status (p<0.001). In the entire population, PFS and OS were significantly associated with TC values both at T0 and T1 (max p=0.002). TC+ pts had significantly worse OS compared to TC- at T0 (HR=2.1 CI=1.1-3.9 p=0.02) and T1 (HR=2.0 CI=1.1-3.6 p=0.03) and worse PFS at T1 (HR=2.9 CI=1.5-5.4 p<0.001). In ER+ pts, TC+ at T0 and T1 associated with worse PFS (HR=2.6 CI=1.2-5.3 p=0.008, and HR=3.8 CI=1.7-8.2 p<0.001) and OS (HR=3.5 CI=1.6-7.6 p=0.001, HR=3.0 CI=1.4-6.1 p=0.002), while in ER- pts TC classes showed no association with outcome. In a small and heterogenous retrospective cohort of mBC pts, MIMESIS-BC showed promising capabilities for prognostic stratification and subtype estimation from liquid biopsy. Validation in an extended prospective cohort is ongoing.
2263P Ethnicity-specific distribution of BRCA1, BRCA2, PALB2 and ATM pathogenic alleles in breast and ovarian cancer patients from the North Caucasus
Authors: E. Imyanitov, E. Bakayeva, L. Sultanova, Z. Khamgokov, M. Chakhkieva, I. Khabriev, M. Murachuev, M. Bolieva, L. Baboshkina, A. Sokolenko
Journal: Annals of Oncology (2023)
2289P Determining anti-cancer efficacy of a reversible LSD1 inhibitor, EXS74539, in primary AML tissues with limited thrombocytopenic effects
Authors: C. Boudesco, R. Okumura, M. lautizi, N. Hieger, V. Thatikonda, M. Ssenekowitsch, T-Y. Lin, G. Fiume, R. Sehlke, T. Winkler-Penz, A. Payne, R. Paveley, G.I. Vladimer
Journal: Annals of Oncology (2023)
Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors
Authors: Ariel A. Hippen, Dalia K. Omran, Lukas M. Weber, Euihye Jung, Ronny Drapkin, Jennifer A. Doherty, Stephanie C. Hicks, Casey S. Greene
Journal: Genome biology (2023)

Single-cell gene expression profiling provides unique opportunities to understand tumor heterogeneity and the tumor microenvironment. Because of cost and feasibility, profiling bulk tumors remains the primary population-scale analytical strategy. Many algorithms can deconvolve these tumors using single-cell profiles to infer their composition. While experimental choices do not change the true underlying composition of the tumor, they can affect the measurements produced by the assay.
Dual AAV-based PCDH15 gene therapy achieves sustained rescue of visual function in a mouse model of Usher syndrome 1F
Authors: Sehar Riaz, Saumil Sethna, Todd Duncan, Muhammad A. Naeem, T. Michael Redmond, Sheikh Riazuddin, Saima Riazuddin, Livia S. Carvalho, Zubair M. Ahmed
Journal: Molecular Therapy (2023)
Remibrutinib demonstrates favorable safety profile and sustained efficacy in chronic spontaneous urticaria over 52 weeks
Authors: Vipul Jain, Ana Giménez-Arnau, Koremasa Hayama, Adam Reich, Warner Carr, Jeffrey Tillinghast, Swapnil Dahale, Karine Lheritier, Pauline Walsh, Artem Zharkov, Sophie Hugot, Sibylle Haemmerle
Journal: Journal of Allergy and Clinical Immunology (2023)

Background Remibrutinib (LOU064), an oral, highly selective Bruton's tyrosine kinase inhibitor (BTKi), offers fast disease control in chronic spontaneous urticaria (CSU) patients who remain symptomatic despite second-generation H1-antihistamines. It is currently in phase 3 development for CSU. Objective To evaluate the long-term safety and efficacy of remibrutinib in CSU patients inadequately controlled with H1-antihistamines. Methods In this phase 2b extension study, patients who completed the core study and had a weekly Urticaria Activity Score (UAS7)≥16 at the beginning of the extension study received remibrutinib 100 mg twice daily for 52 weeks. The primary objective was to assess long-term safety and tolerability. Key efficacy endpoints included change from baseline in UAS7 and proportion of patients with complete response to treatment (UAS7=0) and well-controlled disease (UAS7≤6) at week 4 and over 52 weeks. Results Overall, 84.3% (194/230) of patients entered the treatment period and received ≥1dose of remibrutinib. The overall safety profile of remibrutinib was comparable between the extension and core studies. Most treatment-emergent adverse events (TEAEs) were mild-to-moderate and considered unrelated to remibrutinib by investigators. The 3 most common TEAEs by system organ class were infections (30.9%), skin and subcutaneous tissue (26.8%), and gastrointestinal disorders (16.5%). At week 4 and 52, mean±standard deviation change from baseline in UAS7 was −17.6±13.40 and −21.8±10.70; UAS7=0 (as observed) was achieved in 28.2% and 55.8%, and UAS7≤6 (as observed) in 52.7% and 68.0% of patients, respectively. Conclusion Remibrutinib demonstrated a consistent favorable safety profile with fast and sustained efficacy for up to 52 weeks in CSU patients.
The several ways to authentically cure Alzheimer’s dementia
Authors: Jeffrey Fessel
Journal: Ageing Research Reviews (2023)

Although drugs may slow its progression, authentic cure of AD has never been accomplished. Here, six approaches are suggested that might achieve genuine cure. The six therapies include: 1) treatments addressing levels of TGF-β and Wnt/β-catenin, that become significantly reduced after MCI transitions to AD, and addressing also the impaired epithelial-to-mesenchymal transition (EMT) in AD's pathogenesis; 2) and 3) are two formulations that address the inadequate counter-responses to initial loss of cognition; 4) treatments addressing the brain cells whose impaired functions result in MCI and dementia; 5) the need for using partner drugs even when a particular drug addresses a single pathogenetic cause such as amyloid deposition; 6) enhancing the likelihood of genuine cure by using combinations of approaches chosen from the foregoing. Briefly, genuine cure of AD is possible; however, since AD denotes not one but multiple, phenotypically similar conditions, no one therapy can be generalized to all cases.
A prospective, multicenter, three-cohort study evaluating contrast-induced acute kidney injury (CI-AKI) in patients with cirrhosis
Authors: Daniela Campion, Paola Ponzo, Alessandro Risso, Paola Caropreso, Gian Paolo Caviglia, Tiziana Sanavia, Francesco Frigo, Silvia Bonetto, Ilaria Giovo, Martina Rizzo, Silvia Martini, Elisabetta Bugianesi, Giulio Mengozzi, Alfredo Marzano, Aldo Manca, Giorgio Maria Saracco, Carlo Alessandria
Journal: Journal of Hepatology (2023)
Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell aging
Authors: Huiwen Zheng, Jan Vijg, Atefeh Taherian Fard, Jessica Cara Mar
Journal: Genome biology (2023)

Single-cell RNA-sequencing (scRNA-seq) technologies enable the capture of gene expression heterogeneity and consequently facilitate the study of cell-to-cell variability at the cell type level. Although different methods have been proposed to quantify cell-to-cell variability, it is unclear what the optimal statistical approach is, especially in light of challenging data structures that are unique to scRNA-seq data like zero inflation.
Perforated Marginal Ulcer, Post Roux-En-Y Surgery without Risk Factors: A Case Report
Authors: Nour K. Sabaneh, Ahmed Maasher, Mustafa Amir Abdul Latif, Nour K. Sabaneh
Journal: International Journal of Surgery (2023)

A marginal ulcer is a commonly occurring complication of Roux-en-Y gastric bypass, with an occurrence rate of up to 16%. However, perforation of such ulcers is rare, affecting approximately 1% of cases and typically manifesting at a later stage. Moreover, risk factors, whether surgical or non-surgical, are present in nearly all patients reported in the literature, with only 0.2% found to have none. This case report focuses on a 32-year-old female patient who presented with severe left-sided abdominal pain. She had a history of undergoing Roux-en-Y surgery two years prior. A CT scan of the abdomen revealed the presence of free air and contrast leak, indicative of a perforated marginal ulcer. The patient subsequently underwent a laparoscopic repair of the marginal ulcer, involving the use of an omental patch. In patients experiencing recurrent abdominal pain, the suspicion of a marginal ulcer should arise, prompting the inclusion of upper endoscopy as part of the diagnostic workup. The feasibility of laparoscopic repair with an omental patch has been demonstrated, and patients are advised to undergo follow-up endoscopy. Doctors should have a high suspicion index for perforation of marginal ulcer with any patient after bariatric surgery despite the absence of risk factors.
Large language models propagate race-based medicine
Authors: Jesutofunmi A. Omiye, Jenna C. Lester, Simon Spichak, Veronica Rotemberg, Roxana Daneshjou
Journal: npj Digital Medicine (2023)

Abstract Large language models (LLMs) are being integrated into healthcare systems; but these models may recapitulate harmful, race-based medicine. The objective of this study is to assess whether four commercially available large language models (LLMs) propagate harmful, inaccurate, race-based content when responding to eight different scenarios that check for race-based medicine or widespread misconceptions around race. Questions were derived from discussions among four physician experts and prior work on race-based medical misconceptions believed by medical trainees. We assessed four large language models with nine different questions that were interrogated five times each with a total of 45 responses per model. All models had examples of perpetuating race-based medicine in their responses. Models were not always consistent in their responses when asked the same question repeatedly. LLMs are being proposed for use in the healthcare setting, with some models already connecting to electronic health record systems. However, this study shows that based on our findings, these LLMs could potentially cause harm by perpetuating debunked, racist ideas.
Genomics for monitoring and understanding species responses to global climate change
Authors: Louis Bernatchez, Anne-Laure Ferchaud, Chloé Suzanne Berger, Clare J. Venney, Amanda Xuereb
Journal: Nature Reviews Genetics (2023)

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change. Species and communities can respond to global climate change by genetically adapting to new environmental conditions, by shifting their range or through phenotypic plasticity. This Review summarizes approaches that apply and integrate omics tools to experimentally investigate, monitor and predict these species responses.
Validation of AGA clinical care pathway and AASLD practice guidance for nonalcoholic fatty liver disease in a prospective cohort of patients with type 2 diabetes
Authors: Veeral Ajmera, Kaleb Tesfai, Erick Sandoval, Scarlett Lopez, Vanessa Cervantes, Egbert Madamba, Ricki Bettencourt, Pinelopi Manousou, Lisa Richards, Rohit Loomba
Journal: Hepatology (2023)

Recently, the American Gastroenterological Association and the American Association for the Study of Liver Diseases developed clinical pathways to evaluate populations at high risk for NAFLD. We assessed the diagnostic performance of the new guidance in a well-phenotyped cohort of patients with Type 2 diabetes mellitus (T2DM).
Letter to the Editor: Contrasting effect of iron supplementation in protoporphyria
Authors: Jasmin Barman-Aksözen, Anna-Elisabeth Minder, Detlef Schuppan, Ulrich Stölzel
Journal: Hepatology (2023)

Barman-Aksözen, Jasmin; Minder, Anna-Elisabeth; Schuppan, Detlef; Stölzel, Ulrich Author Information
Reply: Iron supplementation in protoporphyrias
Authors: Cynthia Levy, Amy K. Dickey, Karl E. Anderson, Sioban B. Keel, Manisha Balwani
Journal: Hepatology (2023)

Levy, Cynthia; Dickey, Amy K.; Anderson, Karl E.; Keel, Sioban B.; Balwani, Manisha Author Information